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No attr assembly compare bug #88

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merged 2 commits into from
May 18, 2016
Merged

No attr assembly compare bug #88

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e712871
Add cluster with an assembly fail
martinghunt May 18, 2016
1d656eb
Stop bug when assembly failed, so assembly_compare was never created
martinghunt May 18, 2016
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1 change: 1 addition & 0 deletions ariba/cluster.py
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Original file line number Diff line number Diff line change
Expand Up @@ -105,6 +105,7 @@ def __init__(self,
self.final_assembly_read_depths = os.path.join(self.root_dir, 'assembly.reads_mapped.bam.read_depths.gz')
self.final_assembly_vcf = os.path.join(self.root_dir, 'assembly.reads_mapped.bam.vcf')
self.samtools_vars_prefix = self.final_assembly_bam
self.assembly_compare = None
self.assembly_compare_prefix = os.path.join(self.root_dir, 'assembly_compare')

self.mummer_variants = {}
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2 changes: 1 addition & 1 deletion ariba/clusters.py
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Expand Up @@ -451,7 +451,7 @@ def _write_catted_genes_matching_refs_fasta(self, outfile):
f = pyfastaq.utils.open_file_write(outfile)

for gene in sorted(self.clusters):
if self.clusters[gene].assembly_compare.gene_matching_ref is not None:
if self.clusters[gene].assembly_compare is not None and self.clusters[gene].assembly_compare.gene_matching_ref is not None:
seq = copy.copy(self.clusters[gene].assembly_compare.gene_matching_ref)
seq.id += '.' + '.'.join([
self.clusters[gene].assembly_compare.gene_matching_ref_type,
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4 changes: 4 additions & 0 deletions ariba/test_run_data/non_coding.fa
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Expand Up @@ -4,3 +4,7 @@ GTGCCCGCCGCCCACGAACGAACTGCGGTGAGATGCTTAGGGAACGCCATCCGAGATCAC
>noncoding2
TCTTTAACTGTTCACGACTGTATCGCGGCTTGCAAATCTTAAGTTCTTCCCAAGCGCGCT
GCGATACAAATCCCAAGTTTAGCGGACAGTTCACGCCGGGTTCTAAGAATGTATGCGTCC
>noncoding3
CTAACTTACTACTATGACTGACTGACTGACTGACTGATCGACTGCTGACATCTGATCGAT
CATCCTGTCGACATCATATCTCGATCGATCGATCGACTGACTGACTGACTGACTGAATCT
CACGTACTGACTCATCATCATCATACTCATCATATCATCGATCGATCATCTGATCTGATG
4 changes: 4 additions & 0 deletions ariba/test_run_data/reads_1.fq
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Expand Up @@ -902,3 +902,7 @@ IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
ATCTTTAACTGTTCACGACTGTATCGCGGCTTGCAAATCTTAAGTTCTTC
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@noncoding3/1
CATCCTGTCGACATCATATCTCGATCGATCGATCGACTGACTGACTGACT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
4 changes: 4 additions & 0 deletions ariba/test_run_data/reads_2.fq
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Expand Up @@ -902,3 +902,7 @@ IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
TCTTAGAACCCGGCGTGAACTGTCCGCTAAACTTGGGATTTGTATCGCAG
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@noncoding3/2
CATCAGATCAGATGATCGATCGATGATATGATGAGTATGATGATGATGAG
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
4 changes: 4 additions & 0 deletions ariba/test_run_data/ref_fasta_to_make_reads_from.fa
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Expand Up @@ -30,3 +30,7 @@ TATCGCGGCTTGCAAATCTTAAGTTCTTCCCAAGCGCGCTGCGATACAAATCCCAAGTTT
AGCGGACAGTTCACGCCGGGTTCTAAGAATGTATGCGTCCGTTCGTTTTGTGCAATTGTC
TCTGTATGGACCAATTGTCTACTGGACCGGTAGAAACATAAACGCTCTCTACTCTTCATG
GCGCTATCGGGGAGGGGGCG
>noncoding3
CTAACTTACTACTATGACTGACTGACTGACTGACTGATCGACTGCTGACATCTGATCGAT
CATCCTGTCGACATCATATCTCGATCGATCGATCGACTGACTGACTGACTGACTGAATCT
CACGTACTGACTCATCATCATCATACTCATCATATCATCGATCGATCATCTGATCTGATG